[
    {
        "name": "Variant_calling",
        "docker_name": "variantcalling",
        "description": null,
        "version": "0.0.1",
        "author": "MBB",
        "input": "raw_reads",
        "steps": [
            {
                "title": "Preprocessing",
                "name": "preprocess",
                "tools": [
                    "fastp",
                    "null"
                ],
                "default": "fastp"
            },
            {
                "title": "Mapping",
                "name": "mapping",
                "tools": [
                    "bwa",
                    "bowtie"
                ],
                "default": "bwa"
            },
            {
                "title": "Mark Duplicates",
                "name": "mark_duplicates",
                "tools": [
                    "Picard_MarkDuplicates",
                    "null"
                ],
                "default": "Picard_MarkDuplicates"
            },
            {
                "title": "Prepare fasta genome for index",
                "name": "prepare_fasta",
                "tools": [
                    "gatk_prepare_fasta"
                ],
                "default": "gatk_prepare_fasta"
            },
            {
                "title": "Indel Realign",
                "name": "indel_realign",
                "tools": [
                    "gatk_IndelRealigner",
                    "null"
                ],
                "default": "gatk_IndelRealigner"
            },
            {
                "title": "Variant calling",
                "name": "variant_calling",
                "tools": [
                    "gatk_haplotype_caller",
                    "bcftools_mpileup_and_call",
                    "deep_variant",
                    "freebayes"
                ],
                "default": "gatk_haplotype_caller"
            }
        ],
        "options": [
            {
                "name": "results_dir",
                "type": "output_dir",
                "value": "\/Results",
                "label": "Results directory: ",
                "volumes": [
                    {
                        "Results": "\/Results"
                    }
                ]
            },
            {
                "name": "genome_fasta",
                "type": "input_file",
                "value": "",
                "label": "Path to reference genome fasta file"
            }
        ],
        "params_equals": [
            {
                "param_A": "genome_fasta",
                "param_B": "mapping__bwa_index_genome_fasta"
            },
            {
                "param_A": "genome_fasta",
                "param_B": "mapping__bowtie_index_genome_fasta"
            }
        ],
        "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/variantcalling",
        "json": "",
        "yaml": "{\n  name: Variant_calling,\n  docker_name: variantcalling,\n  description: ,\n  version: \"0.0.1\",\n  author: \"MBB\",\n  input: raw_reads,\n  steps:\n    [\n        { title: Preprocessing, name: preprocess, tools: [fastp, \"null\"], default: fastp },\n        { title: Mapping, name: mapping, tools: [bwa, bowtie], default: bwa },\n        { title: Mark Duplicates, name: mark_duplicates, tools: [Picard_MarkDuplicates, \"null\"], default: Picard_MarkDuplicates },\n        { title: Prepare fasta genome for index, name: prepare_fasta, tools: [gatk_prepare_fasta], default: gatk_prepare_fasta },\n        { title: Indel Realign, name: indel_realign, tools: [gatk_IndelRealigner, \"null\"], default: gatk_IndelRealigner },\n        { title: Variant calling, name: variant_calling, tools: [gatk_haplotype_caller, bcftools_mpileup_and_call, deep_variant, freebayes], default: gatk_haplotype_caller }\n    ],\n  options:\n    [\n      {\n        name: \"results_dir\",\n        type: \"output_dir\",\n        value: \"\/Results\",\n        label: \"Results directory: \",\n        volumes:  [Results: \"\/Results\"]\n      },\n      {\n        name: genome_fasta,\n        type: input_file,\n        value: \"\",\n        label: \"Path to reference genome fasta file\",\n      },\n    ],\n    params_equals: [\n      { param_A: genome_fasta, param_B: mapping__bwa_index_genome_fasta },\n      { param_A: genome_fasta, param_B: mapping__bowtie_index_genome_fasta },\n    ]\n}\n"
    }
]